GSM6932827: HCC827 cells, 2; Homo sapiens; OTHER
We extract genomic DNA from the cultured cells following the manufacture's protocol (The QIAamp DNA Mini Kit (cat. nos. 51304 and 51306) ). For each sample, two libraries were generated: a library derived from 5hmC-enriched reads and a library derived from input-unenriched DNA. Fragmented DNA was normalized to 20 ng total input for each assay and ligated to sequencing adapters. Adapter ligated products were either prepared for whole-genome sequencing using the KAPA Hyper Prep kit (Roche, Switzerland) according to the manufacturer's instructions or 5hmC bases were biotinylated via a two-step chemistry and subsequently enriched by binding to Dynabeads M270 Streptavidin (Thermo Fisher Scientific). All libraries were quantified using a Qubit dsDNA High-Sensitivity Assay (Thermo Fisher Scientific) and normalized in preparation for sequencing. Fragment size profiles of sequencing libraries were verified with the Bioanalyzer dsDNA High-Sensitivity assay (Agilent Technologies) prior to sequencing.